skip to main content
OSTI.GOV title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: MEP pathway products allosterically promote monomerization of deoxy-D-xylulose-5-phosphate synthase to feedback-regulate their supply

Journal Article · · Plant Communications
 [1];  [2];  [3];  [4];  [4];  [3];  [5]; ORCiD logo [1];  [6]
  1. Consejo Superior de Investigaciones Cientificas (CSIC), Valencia (Spain). Univ. Politecnica de Valencia (CSIC-UPV); Consejo Superior de Investigaciones Cientificas (CSIC), Barcelona (Spain). Univ. Autònoma de Barcelona (CSIC-UAB)
  2. Consejo Superior de Investigaciones Cientificas (CSIC) (Spain). Univ. de Zaragoza (GBsC-CSIC)
  3. Joint BioEnergy Institute (JBEI), Emeryville, CA (United States); Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
  4. Nostrum Biodiscovery SL, Barcelona (Spain)
  5. Consejo Superior de Investigaciones Cientificas (CSIC) (Spain). Univ. de Zaragoza (GBsC-CSIC); Inst. de Investigación Sanitaria Aragón (IISA); Biomedical Research Networking Center in Hepatic and Digestive Diseases (CIBEREHD), Madrid (Spain)
  6. Consejo Superior de Investigaciones Cientificas (CSIC), Barcelona (Spain). Univ. Autònoma de Barcelona (CSIC-UAB)
+ Show Author Affiliations

Isoprenoids are a very large and diverse family of metabolites required by all living organisms. All isoprenoids derive from the double-bond isomers isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP), which are produced by the methylerythritol 4-phosphate (MEP) pathway in bacteria and plant plastids. It has been reported that IPP and DMAPP feedback-regulate the activity of deoxyxylulose 5-phosphate synthase (DXS), a dimeric enzyme that catalyzes the main flux-controlling step of the MEP pathway. Here we provide experimental insights into the underlying mechanism. Isothermal titration calorimetry and dynamic light scattering approaches showed that IPP and DMAPP can allosterically bind to DXS in vitro, causing a size shift. In silico ligand binding site analysis and docking calculations identified a potential allosteric site in the contact region between the two monomers of the active DXS dimer. Modulation of IPP and DMAPP contents in vivo followed by immunoblot analyses confirmed that high IPP/DMAPP levels resulted in monomerization and eventual aggregation of the enzyme in bacterial and plant cells. Loss of the enzymatically active dimeric conformation allows a fast and reversible reduction of DXS activity in response to a sudden increase or decrease in IPP/DMAPP supply, whereas aggregation and subsequent removal of monomers that would otherwise be available for dimerization appears to be a more drastic response in the case of persistent IPP/DMAPP overabundance (e.g., by a blockage in their conversion to downstream isoprenoids). Our results represent an important step toward understanding the regulation of the MEP pathway and rational design of biotechnological endeavors aimed at increasing isoprenoid contents in microbial and plant systems.

Research Organization:
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
Sponsoring Organization:
USDOE Office of Science (SC), Biological and Environmental Research (BER)
Grant/Contract Number:
AC02-05CH11231
OSTI ID:
2229049
Journal Information:
Plant Communications, Vol. 4, Issue 3; ISSN 2590-3462
Publisher:
Cell PressCopyright Statement
Country of Publication:
United States
Language:
English

References (45)

Differential Subplastidial Localization and Turnover of Enzymes Involved in Isoprenoid Biosynthesis in Chloroplasts journal February 2016
Enzyme Kinetics by Isothermal Titration Calorimetry: Allostery, Inhibition, and Dynamics journal October 2020
Network Analysis of the MVA and MEP Pathways for Isoprenoid Synthesis journal April 2013
Crystal Structure of 1-Deoxy-d-xylulose 5-Phosphate Synthase, a Crucial Enzyme for Isoprenoids Biosynthesis journal November 2006
Rapid Regulation of the Methylerythritol 4-Phosphate Pathway during Isoprene Synthesis journal August 2004
Breaking new ground in the regulation of the early steps of plant isoprenoid biosynthesis journal June 2015
Deoxyxylulose 5-Phosphate Synthase Controls Flux through the Methylerythritol 4-Phosphate Pathway in Arabidopsis journal July 2014
From feedback inhibition to allostery: the enduring example of aspartate transcarbamoylase journal September 2013
Cholesterol-mediated allosteric regulation of the mitochondrial translocator protein structure journal March 2017
A new family of enzymes catalyzing the first committed step of the methylerythritol 4-phosphate (MEP) pathway for isoprenoid biosynthesis in bacteria journal July 2010
A mutant pyruvate dehydrogenase E1 subunit allows survival of Escherichia coli strains defective in 1-deoxy- d -xylulose 5-phosphate synthase journal January 2006
Post-translational events and modifications regulating plant enzymes involved in isoprenoid precursor biosynthesis journal April 2013
Metabolic Flux Analysis of Plastidic Isoprenoid Biosynthesis in Poplar Leaves Emitting and Nonemitting Isoprene journal March 2014
Feedback Inhibition of Deoxy-d-xylulose-5-phosphate Synthase Regulates the Methylerythritol 4-Phosphate Pathway journal April 2013
Adaptation of hydroxymethylbutenyl diphosphate reductase enables volatile isoprenoid production journal March 2020
Engineering of Recombinant Poplar Deoxy-D-Xylulose-5-Phosphate Synthase (PtDXS) by Site-Directed Mutagenesis Improves Its Activity journal August 2016
PfClpC Is an Essential Clp Chaperone Required for Plastid Integrity and Clp Protease Stability in Plasmodium falciparum journal November 2017
Observation of Thiamin-Bound Intermediates and Microscopic Rate Constants for Their Interconversion on 1-Deoxy- d -xylulose 5-Phosphate Synthase: 600-Fold Rate Acceleration of Pyruvate Decarboxylation by d -Glyceraldehyde-3-phosphate. journal October 2012
An engineered extraplastidial pathway for carotenoid biofortification of leaves journal March 2021
X-ray crystallography–based structural elucidation of enzyme-bound intermediates along the 1-deoxy-d-xylulose 5-phosphate synthase reaction coordinate journal June 2019
Enzyme Inhibitor Studies Reveal Complex Control of Methyl-D-Erythritol 4-Phosphate (MEP) Pathway Enzyme Expression in Catharanthus roseus journal May 2013
Carotenoid accumulation in bacteria with enhanced supply of isoprenoid precursors by upregulation of exogenous or endogenous pathways journal May 2008
Investigation of the methylerythritol 4-phosphate pathway for microbial terpenoid production through metabolic control analysis journal November 2019
Specific Hsp100 Chaperones Determine the Fate of the First Enzyme of the Plastidial Isoprenoid Pathway for Either Refolding or Degradation by the Stromal Clp Protease in Arabidopsis journal January 2016
Negative regulation of plastidial isoprenoid pathway by herbivore-induced β-cyclocitral in Arabidopsis thaliana journal March 2021
Temporal Proteomics of Inducible RNAi Lines of Clp Protease Subunits Identifies Putative Protease Substrates journal December 2017
Overexpression of endogenous 1-deoxy-d-xylulose 5-phosphate synthase (DXS) in cyanobacterium Synechocystis sp. PCC6803 accelerates protein aggregation journal May 2017
Elucidation of the Methylerythritol Phosphate Pathway for Isoprenoid Biosynthesis in Bacteria and Plastids. A Metabolic Milestone Achieved through Genomics journal November 2002
Structural basis of substrate recognition and thermal protection by a small heat shock protein journal May 2021
Epik: a software program for pK a prediction and protonation state generation for drug-like molecules journal September 2007
Arabidopsis J-Protein J20 Delivers the First Enzyme of the Plastidial Isoprenoid Pathway to Protein Quality Control journal October 2013
Guarding the gateway to histidine biosynthesis in plants: Medicago truncatula ATP-phosphoribosyltransferase in relaxed and tense states journal August 2018
Mathematical modelling of the diurnal regulation of the MEP pathway in Arabidopsis journal January 2015
Control of plastidial metabolism by the Clp protease complex journal December 2018
Exploration of the 1-deoxy-d-xylulose 5-phosphate synthases suitable for the creation of a robust isoprenoid biosynthesis system journal March 2017
Conformational dynamics of 1-deoxy-d-xylulose 5-phosphate synthase on ligand binding revealed by H/D exchange MS journal August 2017
Agonist-induced dimer dissociation as a macromolecular step in G protein-coupled receptor signaling journal August 2017
New Method for Fast and Accurate Binding-site Identification and Analysis journal February 2007
Modification of PATase by L/F-transferase generates a ClpS-dependent N-end rule substrate in Escherichia coli journal May 2009
Active Site Histidines Link Conformational Dynamics with Catalysis on Anti-Infective Target 1-Deoxy-d-xylulose 5-Phosphate Synthase journal November 2019
Integrated analysis of isopentenyl pyrophosphate (IPP) toxicity in isoprenoid-producing Escherichia coli journal May 2018
Interference with Clp protease impairs carotenoid accumulation during tomato fruit ripening journal January 2018
The structural basis of allosteric regulation in proteins journal March 2009
Methylerythritol 4-phosphate (MEP) pathway metabolic regulation journal January 2014
Disrupting the Constitutive, Homodimeric Protein–Protein Interface in CK2β Using a Biophysical Fragment-Based Approach journal October 2016

Similar Records

Synthetic Routes to Methylerythritol Phosphate Pathway Intermediates and Downstream Isoprenoids
Journal Article · Tue Jul 01 00:00:00 EDT 2014 · Current Organic Chemistry · OSTI ID:2229049
Crystal Structure of 1-Deoxy-D-xylulose 5-Phosphate Synthase, A Crucial Enzyme for Isoprenoids Biosynthesis
Journal Article · Mon Jan 01 00:00:00 EST 2007 · Journal of Biological Chemistry · OSTI ID:2229049
+1 more
Isopentenyl diphosphate (IPP)-bypass mevalonate pathways for isopentenol production
Journal Article · Thu Dec 17 00:00:00 EST 2015 · Metabolic Engineering · OSTI ID:2229049
+3 more

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
isoprenoids
DXS
feedback regulation
allosteric
monomerization